The impact of mitochondrial protein acetylation status on neuronal function and vulnerability to neurological disorders is unknown. We found that the mitochondrial protein deacetylase SIRT3 mediates adaptive responses of neurons to bioenergetic, oxidative, and excitatory stress. Cortical neurons lacking SIRT3 exhibit heightened sensitivity to glutamate-induced calcium overload and excitotoxicity and oxidative and mitochondrial stress; AAV-mediated Sirt3 gene delivery restores neuronal stress resistance. In models relevant to Huntington's disease and epilepsy, Sirt3(-/-) mice exhibit increased vulnerability of striatal and hippocampal neurons, respectively. SIRT3 deficiency results in hyperacetylation of several mitochondrial proteins, including superoxide dismutase 2 and cyclophilin D. Running wheel exercise increases the expression of Sirt3 in hippocampal neurons, which is mediated by excitatory glutamatergic neurotransmission and is essential for mitochondrial protein acetylation homeostasis and the neuroprotective effects of running. Our findings suggest that SIRT3 plays pivotal roles in adaptive responses of neurons to physiological challenges and resistance to degeneration. Intermittent food deprivation/fasting (IF) improves mood and cognition and protects neurons against excitotoxic degeneration in animal models of epilepsy and Alzheimers disease (AD). The mechanisms by which neuronal networks adapt to IF and how such adaptations impact neuropathological processes are unknown. We found that hippocampal neuronal networks adapt to IF by enhancing GABAergic tone, which is associated with reduced anxiety-like behaviors. These adaptations involve increased expression of the mitochondrial protein deacetylase SIRT3 and are abolished in SIRT3-deficient mice, demonstrating a pivotal role for mitochondrial protein deacetylation in behavioral and neuronal network adaptations to IF. In the AppNL-G-F mouse model of AD, IF reduces neuronal network hyperexcitability and ameliorates deficits in cognition and hippocampal synaptic plasticity. These findings demonstrate a pivotal role for mitochondrial protein deacetylation in behavioral and neuronal network adaptations to IF, and suggest a potential application of intermittent fasting in neurological disorders that involve hyperactivity of neuronal networks.